Gene detail

Detailed information of OS493_005518-T1 in Lophelia pertusa

Genomic Location: scaffold_11:2112029...2115078
NR annotation: KAJ7365411.1, hypothetical protein OS493_005518 [Desmophyllum pertusum]
Species Lophelia pertusa · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q00059	Transcription factor A, mitochondrial OS=Homo sapiens OX=9606 GN=TFAM PE=1 SV=1
Q5D144	Transcription factor A, mitochondrial OS=Sus scrofa OX=9823 GN=TFAM PE=2 SV=1
Q91ZW1	Transcription factor A, mitochondrial OS=Rattus norvegicus OX=10116 GN=Tfam PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005750 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00505 all species →	HMG_box	HMG (high mobility group) box	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036910 all species →	Homologous_superfamily	High mobility group box domain superfamily	Interproscan
IPR051762 all species →	Family	Upstream Binding Factor 1	Interproscan
IPR009071 all species →	Domain	High mobility group box domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR46318 all species →	UPSTREAM BINDING TRANSCRIPTION FACTOR	Interproscan

Gene Ontology

No Gene Ontology signature was detected for OS493_005518-T1. This gene does have a gene model — the search simply returned no hit.

Search by domain instead of by gene. Any accession above (InterPro, Pfam, PANTHER, GO, KEGG) can be used as a query on the Functional Domain Search page, which searches all 148 annotated genomes at once.

KEGG pathway

No KEGG orthology assignment for OS493_005518-T1.

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of OS493_005518-T1 across 110 RNA-seq samples of Lophelia pertusa. Values are TPM (transcripts per million) from the StringTie quantification; one bar is one sample, grouped and coloured by condition, sorted by expression within each group.

110Samples

110TPM > 0

7Conditions

26.9Max TPM

7.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	9.24	15.56
polyp at pH7 6	18	18	9.98	14.86
coral polyp · control treatment	16	16	7.64	16.25
coral polyp · oil and dispersant treatment	16	16	4.55	11.44
coral polyp · oil treatment	16	16	9.56	26.94
coral polyp · dispersant treatment	16	16	4.23	9.64
Polyp	10	10	6.32	10.11

Per sample · hover a bar for the full sample record · show / hide the sample table

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.56
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.72
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.63
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.38
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.00
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.30
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.01
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.94
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.59
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.99
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.62
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.18
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.03
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.68
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.66
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.87
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.20
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.03
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.86
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.55
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.51
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.87
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.22
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.30
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.06
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.79
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.32
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.12
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.92
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.84
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.98
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.68
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.88
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.81
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.22
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.65
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.25
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.48
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.19
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.19
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.64
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.19
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.41
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.68
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.43
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.23
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.87
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.35
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.08
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.79
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.45
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.06
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.44
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.32
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.04
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.13
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.06
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.69
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.16
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.33
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.28
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.92
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.46
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.37
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.62
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.29
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.92
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.69
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.94
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.39
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.49
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.38
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.02
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.89
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.89
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.90
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.38
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.01
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.72
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.55
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.97
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.17
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.06
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.26
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.64
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.45
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.20
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.71
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.54
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.18
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.92
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.41
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.30
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.61
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.00
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.26
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.93
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.63
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.48
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.36
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	10.11
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	9.72
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	9.68
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	9.17
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	7.87
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	6.77
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	3.11
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	2.62
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	2.40
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	1.70

Source: CnidoSite RNA-seq expression matrices (LPERT_TPM, StringTie quantification over 110 runs), joined to SRA sample metadata. Samples whose tissue/treatment is not recorded in the source metadata are grouped by the descriptor carried in the expression matrix itself.